While you're definitely right about the trend evident in that particular game, I have some additional information that I'd like to clarify.
Firstly, it is important to remember that Boss Bass is named Kyodai Pukupuku
(巨大プクプク) in Japan.
The enemy you see there is actually not Boss Bass, but a similar one named Bakubaku
(バクバク) in Japan and "Bubba" by Nintendo Power.
"Bubba" would indeed later be redesigned to look like a carbon copy of Boss Bass in SM64DS, making his redundancy all the more evident. However, he'd later reappear in New Super Mario Bros.
where they gave him a more distinct purple color. Granted, it's not as
distinct as the yellow fish with glasses but at least he doesn't look like a generic Cheep-Cheep anymore. Nintendo Power must've thought he was a new enemy or something, because they ended up renaming him "Cheep-Chomp" in this game.
Speaking of Cheep-Cheeps, their appearances on the N64 is the most unique they've ever looked, being yellow with bright orange fins and goggles (like a Blurp). They looked unique enough that Nintendo Power apparently thought they were a new enemy entirely and named them "Bub". It took until Mario Party 3 for NoA to get their name right. Naturally, in SM64DS they appear with their bog standard red-with-white fins design, which is kind of a bummer.